Commit ab9c6bcd authored by Thomas Shatwell's avatar Thomas Shatwell
Browse files

Added new function profile2grid.R

parent 3034ad9f
#' @title Interpolation of sonde profiles to a grid of fixed depths
#' @description Interpolates vertical profile data (typically from a sonde or profiling system) to defined depths.
#' It uses `data.table` to more quickly and efficiently process large datasets.
#' @param data A data.frame containing the profile data to interpolate, containing columns of at least datetime, depth and values.
#' @param datetime The name of the column containing the datetimes (character).
#' @param depth The name of the column containing the depths (character).
#' @param value The name of the column containing values to be interpolated (character).
#' @param outdepths The interpolation depths, which defines the desired vertical grid (numeric vector). If `NULL`, the function tries to choose suitable depths.
#' @param rule The rule defining how to interpolate outside the data range, as defined in the function \code{approxfun()} function.
#' Copied again: an integer (of length 1 or 2) describing how interpolation is to take place outside the interval [min(x), max(x)].
#' If rule is 1 then NAs are returned for such points and if it is 2, the value at the closest data extreme is used.
#' Use, e.g., rule = 2:1, if the left and right side extrapolation should differ.
#' @param dropNAs Should bad profiles be dropped (`TRUE`) or retained as NAs (`FALSE`) (logical).
#' @details
#' The function takes as input a table in long format, with columns for a timestamp, depth, and measured values.
#' The input data is typically data of multiple profiles from a sonde with one measurement in each row.
#' Each measurement requires a timestamp (`datetime`) that uniquely associates it to a profile.
#' In principle the `datetime` column could contain anything that uniquely identifies each profile, but this is commonly a timestamp.
#' Therefore the times from raw sonde data may need to be `cut()` first. Profiles with less than 5 non-NA values are not interpolated.
#' @return A `matrix` containing the interpolated profile data, nrow = the length of outdepths, and ncol=the number of profiles.
#' The attributes contain some details including the `outdepths` and unique `datetimes`.
#' @author Tom Shatwell
#' @examples
#' \dontrun{
#' out <- profile2grid(...)
#' }
#' @export
profile2grid <- function(data, datetime, depth, value,
outdepths=NULL, rule=c(2,1),
dropNAs=FALSE) {
# require(data.table)
dat <- data.table::copy(data[,c(datetime,depth,value)])
names(dat) <- c("dt", "dep", "val")
data.table::setDT(dat, key = "dt")
dates <- unique(dat[,dt])
if(is.null(outdepths)) {
nodes <- c(0.1,0.2,0.25,0.5,1,2,5,10,20,50,100)
dz <- diff(dat[,dep])
dz <- nodes[which.min(abs(nodes-mean(dz[dz>0], na.rm=TRUE)))]
min_d <- min(dat[,dep], na.rm=TRUE)
max_d <- max(dat[,dep], na.rm=TRUE)
outdepths <- seq(max(min_d%/%dz * dz,0), max_d%/%dz * dz, dz)
# wrapper function to deal with errors
wrapper <- function(p, fn, ...) {
out <- NULL
out <- fn(p, ...)
}, warning=function(x) {
out <<- as.character(x)
}, error=function(x) {
out <<- as.character(x)
isValid <- function(x) {is.numeric(x)}
func <- function(y) {
dat[dt==y, if(sum(!<5) {
stop("Not enough non-NA values to interpolate")
} else {
approx(x = dep, y = val, xout = ..outdepths, rule=rule)$y
out <- lapply(X=dates, FUN = wrapper, fn=func)
retain <- which(sapply(out, isValid)) # which files were successfully read?
drop <- which(!(1:length(dates)) %in% retain)
out[drop] <- rep(list(rep(NA, length(outdepths))), length(drop))
out <- matrix(unlist(out),nrow = length(outdepths))
attributes(out)$outdepths <- outdepths
attributes(out)$dt <- dates
attributes(out)$value <- value
attributes(out)$NA_profiles <- dates[drop]
if(length(drop) > 0) { # print profiles that were not successful as warning
warning(c("Could not interpolate ", length(drop),
" (of ", length(dates),") profiles:\n",
if(dropNAs) {
out <- out[,retain]
attirbutes(out)$dt <- dates[retain]
# return(list(out=matrix(unlist(out),nrow = length(outdepths)),
# dt=dates, depth=outdepths, name=value))
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